We have developed an electron-activated dissociation (EAD) device with product isolation functionality for multistage tandem mass spectrometry (MSn). The EAD portion is a branched magneto-radio freque...

Mass spectrometry-driven non-targeted screening is revealing previously undetected PFAS in food, water, and the environment

We present an optimized electron activated dissociation (EAD) methodology, based on hot electron capture dissociation, for liquid chromatography-tande…

Hear from industry experts about the latest advancements in mass spectrometry

Hear from industry experts about the latest advancements in mass spectrometry

Apply for Territory Manager, Mass Spectrometry - New Jersey job with Danaher in Newark, New Jersey, United States of America. Sales at Danaher

Recently, deep-learning-based in silico spectral libraries have gained increasing attention. Several data-independent acquisition (DIA) software tools have integrated this feature, known as a library-free search, thereby making DIA analysis more accessible. However, controlling the false discovery rate (FDR) is challenging owing to the vast amount of peptide information in in silico libraries. In this study, we introduced a stringent method to evaluate FDR control using DIA software. Recombinant proteins were synthesized from full-length human cDNA libraries and analyzed by using liquid chromatography–mass spectrometry and DIA software. The results were compared with known protein sequences to calculate the FDR. Notably, we compared the identification performance of DIA-NN versions 1.8.1, 1.9.2, and 2.1.0. Versions 1.9.2 and 2.10 identified more peptides than version 1.8.1, and versions 1.9.2 and 2.1.0 used a more conservative identification approach, thus significantly improving the FDR control. Across the synthesized recombinant protein mixtures, the average FDR at the precursor level was 0.538% for version 1.8.1, 0.389% for version 1.9.2, and 0.385% for version 2.1.0; at the protein level, the FDRs were 2.85%, 1.81%, and 1.81%, respectively. Collectively, our data set provides valuable insights for comparing FDR controls across DIA software and aiding bioinformaticians in enhancing their tools.

In this article, data-dependent acquisition (DDA) experimental data collected by the ZenoTOF 8600 system was analyzed with MS-DIAL 5.5 software to detect and

Proteomic experiments, particularly those addressing dynamic proteome properties, time series, or genetic diversity, require the analysis of large sample numbers. Despite significant advancements in p...

Top-down proteomics is the study of intact proteins and their post-translational modifications with mass spectrometry. Historically, this field is more challenging than its bottom-up counterpart because the species are much bigger and have a larger number of possible combinations of sequences and modifications; thus, there is a great need for technological development. With improvements in instrumentation and a multiplicity of fragmentation modes available, top-down proteomics is quickly gaining in popularity with renewed attention on increasing confidence in identification and quantification. Here, we systematically evaluated the Sciex ZenoTOF 7600 system for top-down proteomics, applying standards in the field to validate the platform and further experimenting with its capabilities in electron-activated dissociation and post-translational modification site localization. The instrument demonstrated robustness in standard proteins for platform QC, as aided by zeno trapping. We were also able to apply this to histone post-translational modifications, achieving high sequence coverage that allowed PTM’s site localization across protein sequences with optimized EAD fragmentation. We demonstrated the ability to analyze proteins spanning the mass range and included analysis of glycosylated proteins. This is a reference point for future top-down proteomics experiments to be conducted on the ZenoTOF 7600 system.